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      Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates


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          Escherichia coli is an important microorganism in the gastrointestinal tract of warm-blooded animals. Commensal populations of E. coli consist of stable genetic isolates, which means that each individual has only one phylogenetic group (phylogroup). We evaluated the frequency of human commensal E. coli phylogroups from 116 people and observed that the majority of isolates belonged to group A. We also evaluated the frequency of phylogroups in wastewater samples and found a strong positive correlation between the phylogroup distribution in wastewater and human hosts. In order to find out if some factors, such as geographical location, and climate could influence the worldwide phylogroup distribution, we performed a meta-analysis of 39 different studies and 24 countries, including different climates, living areas, and feeding habits. Unexpectedly, our results showed no substructuring patterns of phylogroups; indicating there was no correlation between phylogroup distribution and geographic location, climate, living area, feeding habits, or date of collection.

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          Standard reference strains of Escherichia coli from natural populations.

          A set of 72 reference strains of Escherichia coli isolated from a variety of hosts and geographical locations has been established for use in studies of variation and genetic structure in natural populations. The strains, which have been characterized by multilocus enzyme electrophoresis, are representative of the range of genotypic variation in the species as a whole.
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            A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

            The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.
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              The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects.

              Escherichia coli was isolated from more than 2300 non-domesticated vertebrate hosts living in Australia. E. coli was most prevalent in mammals, less prevalent in birds and uncommon in fish, frogs and reptiles. Mammals were unlikely to harbour E. coli if they lived in regions with a desert climate and less likely to have E. coli if they lived in the tropics than if they lived in semi-arid or temperate regions. In mammals, the likelihood of isolating E. coli from an individual depended on the diet of the host and E. coli was less prevalent in carnivores than in herbivores or omnivores. In both birds and mammals, the probability of isolating E. coli increased with the body mass of the host. Hosts living in close proximity to human habitation were more likely to harbour E. coli than hosts living away from people. The relative abundance of E. coli groups A, B1, B2 and D strains in mammals depended on climate, host diet and body mass. Group A strains were uncommon, but were isolated from both ectothermic and endothermic vertebrates. Group B1 strains could also be isolated from any vertebrate group, but were predominant in ectothermic vertebrates, birds and carnivorous mammals. Group B2 strains were unlikely to be isolated from ectotherms and were most abundant in omnivorous and herbivorous mammals. Group D strains were rare in ectotherms and uncommon in endotherms, but were equally abundant in birds and mammals. The results of this study suggest that, at the species level, the ecological niche of E. coli is mammals with hindgut modifications to enable microbial fermentation, or in the absence of a modified hindgut, E. coli can only establish a population in 'large-bodied' hosts. The non-random distribution of E. coli genotypes among the different host groups indicates that strains of the four E. coli groups may differ in their ecological niches and life-history characteristics.

                Author and article information

                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                21 December 2017
                : 8
                [1] 1Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas , Campinas, Brazil
                [2] 2Núcleo de Pesquisa em Biodiversidade e Computação (BioComp-USP)-Universidade de São Paulo , São Paulo, Brazil
                [3] 3Secretaria de Estado de Saúde de Mato Grosso , Cuiabá, Brazil
                [4] 4Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo , São Paulo, Brazil
                [5] 5Departamento de Análises Ambientais, Companhia Ambiental do Estado de São Paulo-CETESB , São Paulo, Brazil
                [6] 6Departamento de Engenharia de Computação e Sistemas Digitais, Escola Politécnica da USP , São Paulo, Brazil
                Author notes

                Edited by: Hongyue Dang, Xiamen University, China

                Reviewed by: Scott H. Harrison, North Carolina Agricultural and Technical State University, United States; Qaisar Mahmood, COMSATS Institute of Information Technology, Pakistan

                *Correspondence: Tatiana T. Torres tttorres@ 123456ib.usp.br

                This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology

                Copyright © 2017 Stoppe, Silva, Carlos, Sato, Saraiva, Ottoboni and Torres.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                : 02 July 2017
                : 04 December 2017
                Page count
                Figures: 13, Tables: 1, Equations: 0, References: 102, Pages: 20, Words: 11306
                Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo 10.13039/501100001807
                Award ID: 2010/15222-0
                Award ID: 2007/55312-6
                Original Research

                Microbiology & Virology
                phylogenetic groups,escherichia coli,multivariate analysis,wastewater,commensal strains


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